Journal articles: 'Intercalated Motif'

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Ruggiero, Emanuela, Sara Lago, Primož Šket, Matteo Nadai, Ilaria Frasson, Janez Plavec, and Sara N. Richter. "A dynamic i-motif with a duplex stem-loop in the long terminal repeat promoter of the HIV-1 proviral genome modulates viral transcription." Nucleic Acids Research 47, no. 21 (October 29, 2019): 11057–68. http://dx.doi.org/10.1093/nar/gkz937.

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Abstract I-motifs are non-canonical nucleic acids structures characterized by intercalated H-bonds between hemi-protonated cytosines. Evidence on the involvement of i-motif structures in the regulation of cellular processes in human cells has been consistently growing in the recent years. However, i-motifs within non-human genomes have never been investigated. Here, we report the characterization of i-motifs within the long terminal repeat (LTR) promoter of the HIV-1 proviral genome. Biophysical and biochemical analysis revealed formation of a predominant i-motif with an unprecedented loop composition. One-dimensional nuclear magnetic resonance investigation demonstrated formation of three G-C H-bonds in the long loop, which likely improve the structure overall stability. Pull-down experiments combined with mass spectrometry and protein crosslinking analysis showed that the LTR i-motif is recognized by the cellular protein hnRNP K, which induced folding at physiological conditions. In addition, hnRNP K silencing resulted in an increased LTR promoter activity, confirming the ability of the protein to stabilize the i-motif-forming sequence, which in turn regulates the LTR-mediated HIV-1 transcription. These findings provide new insights into the complexity of the HIV-1 virus and lay the basis for innovative antiviral drug design, based on the possibility to selectively recognize and target the HIV-1 LTR i-motif.

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Canalia, Muriel, and Jean-Louis Leroy. "[5mCCTCTCTCC]4: An i-Motif Tetramer with Intercalated T•T Pairs." Journal of the American Chemical Society 131, no. 36 (September 16, 2009): 12870–71. http://dx.doi.org/10.1021/ja903210t.

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Schumacher, Maria A., and Wenjie Zeng. "Structures of the activator ofK. pneumoniabiofilm formation, MrkH, indicates PilZ domains involved in c-di-GMP and DNA binding." Proceedings of the National Academy of Sciences 113, no. 36 (August 22, 2016): 10067–72. http://dx.doi.org/10.1073/pnas.1607503113.

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The pathogenesis ofKlebsiella pneumoniais linked to the bacteria’s ability to form biofilms. Mannose-resistantKlebsiella-like (Mrk) hemagglutinins are critical forK.pneumoniabiofilm development, and the expression of the genes encoding these proteins is activated by a 3′,5′-cyclic diguanylic acid (c-di-GMP)–regulated transcription factor, MrkH. To gain insight into MrkH function, we performed structural and biochemical analyses. Data revealed MrkH to be a monomer with a two-domain architecture consisting of a PilZ C-domain connected to an N domain that unexpectedly also harbors a PilZ-like fold. Comparison of apo- and c-di-GMP–bound MrkH structures reveals a large 138° interdomain rotation that is induced by binding an intercalated c-di-GMP dimer. c-di-GMP interacts with PilZ C-domain motifs 1 and 2 (RxxxR and D/NxSxxG) and a newly described c-di-GMP–binding motif in the MrkH N domain. Strikingly, these c-di-GMP–binding motifs also stabilize an open state conformation in apo MrkH via contacts from the PilZ motif 1 to residues in the C-domain motif 2 and the c-di-GMP–binding N-domain motif. Use of the same regions in apo structure stabilization and c-di-GMP interaction allows distinction between the states. Indeed, domain reorientation by c-di-GMP complexation with MrkH, which leads to a highly compacted structure, suggests a mechanism by which the protein is activated to bind DNA. To our knowledge, MrkH represents the first instance of specific DNA binding mediated by PilZ domains. The MrkH structures also pave the way for the rational design of inhibitors that targetK.pneumoniabiofilm formation.

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Lee, Gyeong Jin, and Tae-il Kim. "pH-Responsive i-motif Conjugated Hyaluronic Acid/Polyethylenimine Complexes for Drug Delivery Systems." Pharmaceutics 11, no. 5 (May 27, 2019): 247. http://dx.doi.org/10.3390/pharmaceutics11050247.

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i-motif is cytosine (C)-rich oligonucleotide (ODN) which shows pH-responsive structure change in acidic condition. Therefore, it has been utilized for the trigger of intercalated drug release, responding to environmental pH change. In this study, 2.76 molecules of i-motif binding ODNs (IBOs) were conjugated to each hyaluronic acid (HA) via amide bond linkages. Synthesis of HA-IBO conjugate (HB) was confirmed by FT-IR and agarose gel electrophoresis with Stains-All staining. After hybridization of HB with i-motif ODN (IMO), it was confirmed that doxorubicin (DOX) could be loaded in HB-IMO hybrid structure (HBIM) with 65.6% of drug loading efficiency (DLE) and 25.0% of drug loading content (DLC). At pH 5.5, prompt and significant DOX release from HBIM was observed due to the disruption of HBIM hybrid structure via i-motif formation of IMO, contrary to pH 7.4 condition. Then, HBIM was complexed with low molecular weight polyethylenimine (PEI1.8k), forming positively charged nanostructures (Z-average size: 126.0 ± 0.4 nm, zeta-potential: 16.1 ± 0.3 mV). DOX-loaded HBIM/PEI complexes displayed higher anticancer efficacy than free DOX in A549 cells, showing the potential for pH-responsive anticancer drug delivery systems.

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Singh, Raghvendra P., Ralf Blossey, and Fabrizio Cleri. "DNA i-motif provides steel-like tough ends to chromosomes." MRS Proceedings 1621 (2014): 135–41. http://dx.doi.org/10.1557/opl.2014.282.

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ABSTRACTWe studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm-long nanowires, based on a repeated TC5 sequence from NMR crystallographic data, fully relaxed and equilibrated in water. The unusual C●C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformations with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young’s and bending moduli of the nanowire, as well as estimates for the tensile strength and persistence length. According to our results, i-motif nanowires share similarities with structural proteins, as far as their tensile stiffness, but are closer to nucleic acids and flexible proteins, as far as their bending rigidity is concerned. Curiously enough, their tensile strength makes such DNA fragments tough as mild steel or a nickel alloy. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.

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Cai, L., L. Chen, S. Raghavan, A. Rich, R. Ratliff, and R. Moyzis. "Intercalated cytosine motif and novel adenine clusters in the crystal structure of the Tetrahymena telomere." Nucleic Acids Research 26, no. 20 (October 1, 1998): 4696–705. http://dx.doi.org/10.1093/nar/26.20.4696.

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Eigenthaler, Martin, Stefan Engelhardt, Birgitta Schinke, Anna Kobsar, Eva Schmitteckert, Stepan Gambaryan, Catherine M. Engelhardt, et al. "Disruption of cardiac Ena-VASP protein localization in intercalated disks causes dilated cardiomyopathy." American Journal of Physiology-Heart and Circulatory Physiology 285, no. 6 (December 2003): H2471—H2481. http://dx.doi.org/10.1152/ajpheart.00362.2003.

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Vasodilator-stimulated phosphoprotein (VASP) and mammalian enabled (Mena) are actin cytoskeleton and signaling modulators. Ena-VASP proteins share an identical domain organization with an NH2-terminal Ena VASP homology (EVH1) domain, which mediates the binding of these proteins to FPPPP-motif containing partners such as zyxin and vinculin. VASP and Mena are abundantly expressed in the heart. However, previous studies showed that disruption by gene targeting of VASP or Mena genes in mice did not reveal any cardiac phenotype, whereas mice lacking both VASP and Mena died during embryonic development. To determine the in vivo function of Ena-VASP proteins in the heart, we used a dominant negative strategy with cardiac-specific expression of the VASP-EVH1 domain. Transgenic mice with cardiac myocyte-restricted, α-myosin heavy chain promoter-directed expression of the VASP-EVH1 domain were generated. Overexpression of the EVH1 domain resulted in specific displacement of both VASP and Mena from cardiac intercalated disks. VASP-EVH1 transgenic mice developed dilated cardiomyopathy with myocyte hypertrophy and bradycardia, which resulted in early postnatal lethality in mice with high levels of transgene expression. The results demonstrate that Ena-VASP proteins may play an important role in intercalated disk function at the interface between cardiac myocytes.

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Chou, Shan-Ho, and Ko-Hsin Chin. "Quadruple intercalated G-6 stack: a possible motif in the fold-back structure of the Drosophila centromeric dodeca-satellite?" Journal of Molecular Biology 314, no. 1 (November 2001): 139–52. http://dx.doi.org/10.1006/jmbi.2001.5131.

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Berger, Imre, ChulHee Kang, April Fredian, Robert Ratliff, Robert Moyzis, and Alexander Rich. "Extension of the four-stranded intercalated cytosine motif by adenine•adenine base pairing in the crystal structure of d(CCCAAT)." Nature Structural & Molecular Biology 2, no. 5 (May 1995): 416–25. http://dx.doi.org/10.1038/nsb0595-416.

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Toye, Ashley M. "Defective kidney anion-exchanger 1 (AE1, Band 3) trafficking in dominant distal renal tubular acidosis (dRTA)." Biochemical Society Symposia 72 (January 1, 2005): 47–63. http://dx.doi.org/10.1042/bss0720047.

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dRTA (distal renal tubular acidosis) results from the failure of the a-intercalated cells in the distal tubule of the nephron to acidify the urine. A truncated form of AE1 (anion-exchanger 1; Band 3), kAE1 (kidney isoform of AE1), is located in the basolateral membrane of the intercalated cell. Mutations in the AE1 gene cause autosomal dominant and recessive forms of dRTA. All the dominant dRTA mutations investigated cause aberrant trafficking of kAE1, resulting in its intracellular retention or mistargeting to the apical plasma membrane. Therefore the intracellular retention of hetero-oligomers containing wild-type and dRTA mutants, or the mistargeted protein in the apical membrane neutralizing acid secretion, explains dominant dRTA. The kAE1 (Arg901→stop) mutant has been studied in more detail, since the mistargeting kAE1 (Arg901→stop) from the basolateral to the apical membrane is consistent with the removal of a basolateral localization signal. The C-terminal amino acids deleted by the Arg901→stop mutation, contain a tyrosine motif and a type II PDZ interaction domain. The tyrosine residue (Tyr904), but not the PDZ domain, is critical for basolateral localization. In the absence of the N-terminus of kAE1, the C-terminus was not sufficient to localize kAE1 to the basolateral membrane. This suggests that a determinant within the kAE1 N-terminus co-operates with the C-terminus for kAE1 basolateral localization. Interestingly, Tyr359, in the N-terminal domain, and Tyr904 in the C-terminus of AE1 are phosphorylated in red blood cells. A potential scheme is suggested where successive phosphorylation of these residues is necessary for correct localization and recycling of kAE1 to the basolateral membrane.

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Masai, Hisao, Naoko Kakusho, Rino Fukatsu, Yue Ma, Keisuke Iida, Yutaka Kanoh, and Kazuo Nagasawa. "Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences." Journal of Biological Chemistry 293, no. 44 (September 14, 2018): 17033–49. http://dx.doi.org/10.1074/jbc.ra118.005240.

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G-quadruplexes (G4s) are four-stranded DNA structures comprising stacks of four guanines, are prevalent in genomes, and have diverse biological functions in various chromosomal structures. A conserved protein, Rap1-interacting factor 1 (Rif1) from fission yeast (Schizosaccharomyces pombe), binds to Rif1-binding sequence (Rif1BS) and regulates DNA replication timing. Rif1BS is characterized by the presence of multiple G-tracts, often on both strands, and their unusual spacing. Although previous studies have suggested generation of G4-like structures on duplex Rif1BS, its precise molecular architecture remains unknown. Using gel-shift DNA binding assays and DNA footprinting with various nuclease probes, we show here that both of the Rif1BS strands adopt specific higher-order structures upon heat denaturation. We observed that the structure generated on the G-strand is consistent with a G4 having unusually long loop segments and that the structure on the complementary C-strand does not have an intercalated motif (i-motif). Instead, we found that the formation of the C-strand structure depends on the G4 formation on the G-strand. Thus, the higher-order structure generated at Rif1BS involved both DNA strands, and in some cases, G4s may form on both of these strands. The presence of multiple G-tracts permitted the formation of alternative structures when some G-tracts were mutated or disrupted by deazaguanine replacement, indicating the robust nature of DNA higher-order structures generated at Rif1BS. Our results provide general insights into DNA structures generated at G4-forming sequences on duplex DNA.

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Benevides, James M., ChulHee Kang, and George J. Thomas. "Raman Signature of the Four-Stranded Intercalated Cytosine Motif in Crystal and Solution Structures of DNA Deoxycytidylates d(CCCT) and d(C8)†." Biochemistry 35, no. 18 (January 1996): 5747–55. http://dx.doi.org/10.1021/bi9529420.

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13

Hee, Chee-Seng, Judith Habazettl, Christoph Schmutz, Tilman Schirmer, Urs Jenal, and Stephan Grzesiek. "Intercepting second-messenger signaling by rationally designed peptides sequestering c-di-GMP." Proceedings of the National Academy of Sciences 117, no. 29 (July 1, 2020): 17211–20. http://dx.doi.org/10.1073/pnas.2001232117.

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The bacterial second messenger cyclic diguanylate (c-di-GMP) regulates a wide range of cellular functions from biofilm formation to growth and survival. Targeting a second-messenger network is challenging because the system involves a multitude of components with often overlapping functions. Here, we present a strategy to intercept c-di-GMP signaling pathways by directly targeting the second messenger. For this, we developed a c-di-GMP–sequestering peptide (CSP) that was derived from a CheY-like c-di-GMP effector protein. CSP binds c-di-GMP with submicromolar affinity. The elucidation of the CSP⋅c-di-GMP complex structure by NMR identified a linear c-di-GMP–binding motif, in which a self-intercalated c-di-GMP dimer is tightly bound by a network of H bonds and π-stacking interactions involving arginine and aromatic residues. Structure-based mutagenesis yielded a variant with considerably higher, low-nanomolar affinity, which subsequently was shortened to 19 residues with almost uncompromised affinity. We demonstrate that endogenously expressed CSP intercepts c-di-GMP signaling and effectively inhibits biofilm formation inPseudomonas aeruginosa, the most widely used model for serious biofilm-associated medical implications.

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Gallego, José, Shan-Ho Chou, and Brian R. Reid. "Centromeric pyrimidine strands fold into an intercalated motif by forming a double hairpin with a Novel T:G:G:T tetrad: solution structure of the d(TCCCGTTTCCA) dimer 1 1Edited by I Tinoco." Journal of Molecular Biology 273, no. 4 (November 1997): 840–56. http://dx.doi.org/10.1006/jmbi.1997.1361.

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Petrunina, N. A., V. V. Lebedev, Yu G. Kirillova, A. V. Aralov, A. M. Varizhuk, and M. V. Sardushkin. "DNA Intercalated Motifs with Non-Nucleoside Inserts." Russian Journal of Bioorganic Chemistry 47, no. 6 (November 2021): 1341–44. http://dx.doi.org/10.1134/s1068162021060212.

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Irving, Kelly L., Jessica J. King, Zoë A. E. Waller, Cameron W. Evans, and Nicole M. Smith. "Stability and context of intercalated motifs (i-motifs) for biological applications." Biochimie 198 (July 2022): 33–47. http://dx.doi.org/10.1016/j.biochi.2022.03.001.

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Baulin, Eugene, Valeriy Metelev, and Alexey Bogdanov. "Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA–protein complexes." Nucleic Acids Research 48, no. 15 (July 20, 2020): 8675–85. http://dx.doi.org/10.1093/nar/gkaa610.

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Abstract Along with nucleobase pairing, base-base stacking interactions are one of the two main types of strong non-covalent interactions that define the unique secondary and tertiary structure of RNA. In this paper we studied two subfamilies of nucleobase-inserted stacking structures: (i) with any base intercalated between neighboring nucleotide residues (base-intercalated element, BIE, i + 1); (ii) with any base wedged into a hydrophobic cavity formed by heterocyclic bases of two nucleotides which are one nucleotide apart in sequence (base-wedged element, BWE, i + 2). We have exploited the growing database of natively folded RNA structures in Protein Data Bank to analyze the distribution and structural role of these motifs in RNA. We found that these structural elements initially found in yeast tRNAPhe are quite widespread among the tertiary structures of various RNAs. These motifs perform diverse roles in RNA 3D structure formation and its maintenance. They contribute to the folding of RNA bulges and loops and participate in long-range interactions of single-stranded stretches within RNA macromolecules. Furthermore, both base-intercalated and base-wedged motifs participate directly or indirectly in the formation of RNA functional centers, which interact with various ligands, antibiotics and proteins.

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Sheng, Qiran, Joseph C. Neaverson, Tasnim Mahmoud, Clare E. M. Stevenson, Susan E. Matthews, and Zoë A. E. Waller. "Identification of new DNA i-motif binding ligands through a fluorescent intercalator displacement assay." Organic & Biomolecular Chemistry 15, no. 27 (2017): 5669–73. http://dx.doi.org/10.1039/c7ob00710h.

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Chen, Xiaorong, Noah P. Bradley, Wei Lu, Katherine L. Wahl, Mei Zhang, Hua Yuan, Xian-Feng Hou, Brandt F. Eichman, and Gong-Li Tang. "Base excision repair system targeting DNA adducts of trioxacarcin/LL-D49194 antibiotics for self-resistance." Nucleic Acids Research 50, no. 5 (February 22, 2022): 2417–30. http://dx.doi.org/10.1093/nar/gkac085.

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Abstract Two families of DNA glycosylases (YtkR2/AlkD, AlkZ/YcaQ) have been found to remove bulky and crosslinking DNA adducts produced by bacterial natural products. Whether DNA glycosylases eliminate other types of damage formed by structurally diverse antibiotics is unknown. Here, we identify four DNA glycosylases—TxnU2, TxnU4, LldU1 and LldU5—important for biosynthesis of the aromatic polyketide antibiotics trioxacarcin A (TXNA) and LL-D49194 (LLD), and show that the enzymes provide self-resistance to the producing strains by excising the intercalated guanine adducts of TXNA and LLD. These enzymes are highly specific for TXNA/LLD-DNA lesions and have no activity toward other, less stable alkylguanines as previously described for YtkR2/AlkD and AlkZ/YcaQ. Similarly, TXNA-DNA adducts are not excised by other alkylpurine DNA glycosylases. TxnU4 and LldU1 possess unique active site motifs that provide an explanation for their tight substrate specificity. Moreover, we show that abasic (AP) sites generated from TxnU4 excision of intercalated TXNA-DNA adducts are incised by AP endonuclease less efficiently than those formed by 7mG excision. This work characterizes a distinct class of DNA glycosylase acting on intercalated DNA adducts and furthers our understanding of specific DNA repair self-resistance activities within antibiotic producers of structurally diverse, highly functionalized DNA damaging agents.

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Alethea, Tabor B. "Synthesis of a peptide-intercalator hybrid based on the bZIP motif from GCN4." Tetrahedron 52, no. 6 (February 1996): 2229–34. http://dx.doi.org/10.1016/0040-4020(95)01053-x.

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Mahajan, Mukesh, Nikhil Bharambe, Yutong Shang, Bin Lu, Abhishek Mandal, Pooja Madan Mohan, Rihua Wang, et al. "NMR identification of a conserved Drp1 cardiolipin-binding motif essential for stress-induced mitochondrial fission." Proceedings of the National Academy of Sciences 118, no. 29 (July 14, 2021): e2023079118. http://dx.doi.org/10.1073/pnas.2023079118.

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Mitochondria form tubular networks that undergo coordinated cycles of fission and fusion. Emerging evidence suggests that a direct yet unresolved interaction of the mechanoenzymatic GTPase dynamin-related protein 1 (Drp1) with mitochondrial outer membrane–localized cardiolipin (CL), externalized under stress conditions including mitophagy, catalyzes essential mitochondrial hyperfragmentation. Here, using a comprehensive set of structural, biophysical, and cell biological tools, we have uncovered a CL-binding motif (CBM) conserved between the Drp1 variable domain (VD) and the unrelated ADP/ATP carrier (AAC/ANT) that intercalates into the membrane core to effect specific CL interactions. CBM mutations that weaken VD–CL interactions manifestly impair Drp1-dependent fission under stress conditions and induce “donut” mitochondria formation. Importantly, VD membrane insertion and GTP-dependent conformational rearrangements mediate only transient CL nonbilayer topological forays and high local membrane constriction, indicating that Drp1–CL interactions alone are insufficient for fission. Our studies establish the structural and mechanistic bases of Drp1–CL interactions in stress-induced mitochondrial fission.

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Weil, Jonathan, Tongpil Min, Cheng Yang, Shuren Wang, Cory Sutherland, Nanda Sinha, and ChulHee Kang. "Stabilization of the i-motif by intramolecular adenine–adenine–thymine base triple in the structure of d(ACCCT)." Acta Crystallographica Section D Biological Crystallography 55, no. 2 (February 1, 1999): 422–29. http://dx.doi.org/10.1107/s0907444998012529.

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The crystal structure of d(ACCCT), solved by molecular replacement, shows a four-stranded i-motif conformation, where two parallel duplexes intercalate with one another in opposite orientations. Each duplex is stabilized by hemi-protonated C–C+ base pairing between parallel strands, and a string of water molecules bridge the cytosine N4 atoms to phosphate O atoms. This structure of d(ACCCT) shows examples of reversed Hoogsteen and Watson–Crick base pairing in both intermolecular and intramolecular manners to stabilize the tetraplex. Noticeably, the four-stranded complex is further stabilized at one end by a three-base hydrogen-bonding network, in which two adenines and a thymine form four hydrogen bonds via a reverse Hoogsteen and an asymmetric adenine–adenine base pairing. The structure of d(ACCCT) shows a similar local structure to that found in the d(TAA) part of the crystal structure of d(TAACCC) and provides further structural evidence that these base arrangements are essential for stabilizing these novel DNA super-secondary structures.

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Warren, Garrett M., Aviv Meir, Juncheng Wang, Dinshaw J. Patel, Eric C. Greene, and Stewart Shuman. "Structure–activity relationships at a nucleobase-stacking tryptophan required for chemomechanical coupling in the DNA resecting motor-nuclease AdnAB." Nucleic Acids Research 50, no. 2 (December 30, 2021): 952–61. http://dx.doi.org/10.1093/nar/gkab1270.

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Abstract Mycobacterial AdnAB is a heterodimeric helicase-nuclease that initiates homologous recombination by resecting DNA double-strand breaks. The AdnB subunit hydrolyzes ATP to drive single-nucleotide steps of 3′-to-5′ translocation of AdnAB on the tracking DNA strand via a ratchet-like mechanism. Trp325 in AdnB motif III, which intercalates into the tracking strand and makes a π stack on a nucleobase 5′ of a flipped-out nucleoside, is the putative ratchet pawl without which ATP hydrolysis is mechanically futile. Here, we report that AdnAB mutants wherein Trp325 was replaced with phenylalanine, tyrosine, histidine, leucine, or alanine retained activity in ssDNA-dependent ATP hydrolysis but displayed a gradient of effects on DSB resection. The resection velocities of Phe325 and Tyr325 mutants were 90% and 85% of the wild-type AdnAB velocity. His325 slowed resection rate to 3% of wild-type and Leu325 and Ala325 abolished DNA resection. A cryo-EM structure of the DNA-bound Ala325 mutant revealed that the AdnB motif III peptide was disordered and the erstwhile flipped out tracking strand nucleobase reverted to a continuous base-stacked arrangement with its neighbors. We conclude that π stacking of Trp325 on a DNA nucleobase triggers and stabilizes the flipped-out conformation of the neighboring nucleoside that underlies formation of a ratchet pawl.

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Palchykov, V., A. Gaponov, N. Manko, N. Finiuk, О. Novikevych, O. Gromyko, R. Stoika, and N. Pokhodylo. "Synthesis of the novel cage amides and imides and evaluation of their antibacterial and antifungal activity." Ukrainian Biochemical Journal 94, no. 3 (October 4, 2022): 68–80. http://dx.doi.org/10.15407/ubj94.03.068.

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Cage amides and imides bearing bicyclo[2.2.1]- and bicyclo[2.2.2]-subunits were synthesized and evaluated both for antimicrobial activity toward five key ESKAPE pathogenic bacteria: one Gram‐positive bacteria methicillin‐resistant Staphylococcus aureus (ATCC 43300), four Gram‐negative bacteria Escherichia coli (ATCC 25922), Klebsiella pneumoniae (ATCC 700603), Acinetobacter baumannii (ATCC 19606) and Pseudomonas aeruginosa (ATCC 27853) and for antifungal activity towards pathogenic fungal strains Candida albicans (ATCC 90028) and Cryptococcus neoformans var. Grubii (H99; ATCC 208821). Compound VP-4539 with bicyclo[2.2.2]octene motif demonstrated the highest cytotoxic activity towards C. neoformans, while human keratinocytes of HaCaT line, murine fibroblasts of Balb/c 3T3 line and mitogen-activated lymphocytes of peripheral human blood were found to be tolerant to its action. VP-4539 compound did not intercalate into salmon sperm DNA indicating that its cytotoxicity is not related to intercalation into nucleic acid. Keywords: antifungal, antimicrobial, bicyclo[2.2.1]heptane, bicyclo[2.2.2]octene, cytotoxicity, DNA intercalation, human keratinocytes, lymphocytes, сage compounds

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El-Sayed, Ahmed A., Erik B. Pedersen, and Nahid A. Khaireldin. "Studying the Influence of the Pyrene Intercalator TINA on the Stability of DNA i-Motifs." Nucleosides, Nucleotides and Nucleic Acids 31, no. 12 (December 2012): 872–79. http://dx.doi.org/10.1080/15257770.2012.742199.

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Wolski, Pawel, Krzysztof Nieszporek, and Tomasz Panczyk. "Cytosine-Rich DNA Fragments Covalently Bound to Carbon Nanotube as Factors Triggering Doxorubicin Release at Acidic pH. A Molecular Dynamics Study." International Journal of Molecular Sciences 22, no. 16 (August 6, 2021): 8466. http://dx.doi.org/10.3390/ijms22168466.

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This works deals with analysis of properties of a carbon nanotube, the tips of which were functionalized by short cytosine-rich fragments of ssDNA. That object is aimed to work as a platform for storage and controlled release of doxorubicin in response to pH changes. We found that at neutral pH, doxorubicin molecules can be intercalated between the ssDNA fragments, and formation of such knots can effectively block other doxorubicin molecules, encapsulated in the nanotube interior, against release to the bulk. Because at the neutral pH, the ssDNA fragments are in form of random coils, the intercalation of doxorubicin is strong. At acidic pH, the ssDNA fragments undergo folding into i-motifs, and this leads to significant reduction of the interaction strength between doxorubicin and other components of the system. Thus, the drug molecules can be released to the bulk at acidic pH. The above conclusions concerning the storage/release mechanism of doxorubicin were drawn from the observation of molecular dynamics trajectories of the systems as well as from analysis of various components of pair interaction energies.

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Koch, Sandra C., Jochen Kuper, Karola L. Gasteiger, Nina Simon, Ralf Strasser, David Eisen, Simon Geiger, Sabine Schneider, Caroline Kisker, and Thomas Carell. "Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)." Proceedings of the National Academy of Sciences 112, no. 27 (June 22, 2015): 8272–77. http://dx.doi.org/10.1073/pnas.1508509112.

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Nucleotide excision repair (NER) is responsible for the removal of a large variety of structurally diverse DNA lesions. Mutations of the involved proteins cause the xeroderma pigmentosum (XP) cancer predisposition syndrome. Although the general mechanism of the NER process is well studied, the function of the XPA protein, which is of central importance for successful NER, has remained enigmatic. It is known, that XPA binds kinked DNA structures and that it interacts also with DNA duplexes containing certain lesions, but the mechanism of interactions is unknown. Here we present two crystal structures of the DNA binding domain (DBD) of the yeast XPA homolog Rad14 bound to DNA with either a cisplatin lesion (1,2-GG) or an acetylaminofluorene adduct (AAF-dG). In the structures, we see that two Rad14 molecules bind to the duplex, which induces DNA melting of the duplex remote from the lesion. Each monomer interrogates the duplex with a β-hairpin, which creates a 13mer duplex recognition motif additionally characterized by a sharp 70° DNA kink at the position of the lesion. Although the 1,2-GG lesion stabilizes the kink due to the covalent fixation of the crosslinked dG bases at a 90° angle, the AAF-dG fully intercalates into the duplex to stabilize the kinked structure.

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Pushkin, Alexander, Natalia Abuladze, Debra Newman, Vladimir Muronets, Pejvak Sassani, Sergei Tatishchev, and Ira Kurtz. "The COOH termini of NBC3 and the 56-kDa H+-ATPase subunit are PDZ motifs involved in their interaction." American Journal of Physiology-Cell Physiology 284, no. 3 (March 1, 2003): C667—C673. http://dx.doi.org/10.1152/ajpcell.00225.2002.

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The electroneutral sodium bicarbonate cotransporter 3 (NBC3) coimmunoprecipitates from renal lysates with the vacuolar H+-ATPase. In renal type A and B intercalated cells, NBC3 colocalizes with the vacuolar H+-ATPase. The involvement of the COOH termini of NBC3 and the 56-kDa subunit of the proton pump in the interaction of these proteins was investigated. The intact and modified COOH termini of NBC3 and the 56-kDa subunit of the proton pump were synthesized, coupled to Sepharose beads, and used to pull down kidney membrane proteins. Both the 56- and the 70-kDa subunits of the proton pump, as well as a PDZ domain containing protein Na+/H+ exchanger regulatory factor 1 (NHERF-1), were bound to the intact 18 amino acid NBC3 COOH terminus. A peptide truncated by five COOH-terminal amino acids did not bind these proteins. Replacement of the COOH-terminal leucine with glycine blocked binding of both the proton pump subunits but did not affect binding of NHERF-1. The 18 amino acid COOH terminus of the 56-kDa subunit of the proton pump bound NHERF-1 and NBC3, but the truncated and modified peptide did not. A complex of NBC3, the 56-kDa subunit of the proton pump, and NHERF-1 was identified in rat kidney. The data indicate that the COOH termini of NBC3 and the 56-kDa subunit of the vacuolar proton pump are PDZ-interacting motifs that are necessary for the interaction of these proteins. NHERF-1 is involved in the interaction of NBC3 and the vacuolar proton pump.

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Bishop, Michael M., Leonard F. Lindoy, Srihari Mahadev, and Peter Turner. "Modification of supramolecular motifs: perturbation of the structure of an extended hydrogen-bonded biuret array by interaction with an intercalated copper complex and methanol molecules †." Journal of the Chemical Society, Dalton Transactions, no. 3 (2000): 233–34. http://dx.doi.org/10.1039/a909359a.

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30

Wu, Hao, Mithun Mitra, M. Nabuan Naufer, Micah J. McCauley, Robert J. Gorelick, Ioulia Rouzina, Karin Musier-Forsyth, and Mark C. Williams. "Differential contribution of basic residues to HIV-1 nucleocapsid protein’s nucleic acid chaperone function and retroviral replication." Nucleic Acids Research 42, no. 4 (November 28, 2013): 2525–37. http://dx.doi.org/10.1093/nar/gkt1227.

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Abstract The human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) protein contains 15 basic residues located throughout its 55-amino acid sequence, as well as one aromatic residue in each of its two CCHC-type zinc finger motifs. NC facilitates nucleic acid (NA) rearrangements via its chaperone activity, but the structural basis for this activity and its consequences in vivo are not completely understood. Here, we investigate the role played by basic residues in the N-terminal domain, the N-terminal zinc finger and the linker region between the two zinc fingers. We use in vitro ensemble and single-molecule DNA stretching experiments to measure the characteristics of wild-type and mutant HIV-1 NC proteins, and correlate these results with cell-based HIV-1 replication assays. All of the cationic residue mutations lead to NA interaction defects, as well as reduced HIV-1 infectivity, and these effects are most pronounced on neutralizing all five N-terminal cationic residues. HIV-1 infectivity in cells is correlated most strongly with NC’s NA annealing capabilities as well as its ability to intercalate the DNA duplex. Although NC’s aromatic residues participate directly in DNA intercalation, our findings suggest that specific basic residues enhance these interactions, resulting in optimal NA chaperone activity.

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Sahr, KE, BP Daniels, and M. Hanspal. "Identification of the proximal erythroid promoter region of the mouse anion exchanger gene." Blood 88, no. 12 (December 15, 1996): 4500–4509. http://dx.doi.org/10.1182/blood.v88.12.4500.bloodjournal88124500.

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The AE1 gene is expressed in erythrocytes and the A-type intercalated cells of the kidney distal collecting duct. Although the 5′ end of the principal transcript expressed in murine erythroid cells has previously been mapped to a cluster of transcription start sites located immediately upstream of exon 1, the 5′ end of the mouse kidney transcript has not been identified. Using the anchored polymerase chain reaction technique to analyze mouse kidney AE1 mRNA, we identified an internal transcription start site located within erythroid intron 3. This site defines an exon of 37 nucleotides that forms the 5′ end of the mouse kidney AE1 transcript. AE1 transcripts beginning at this internal start site could not be detected in RNA isolated from purified erythroid progenitor cells or from erythroid cells undergoing erythropoietin-dependent terminal maturation, although transcripts derived from the upstream site were abundant, indicating that only the upstream promoter is active during erythropoiesis. Transient expression of reporter constructs in erythroid and nonerythroid cell lines identified a proximal upstream region of approximately 135 nucleotides that was active as a basal promoter. However, an additional approximately 200 nucleotides of upstream sequence was required for induced levels of activity in erythroid cells. Although our functional approach does not yet indicate the precise sequences required for erythroid induction, the AE1 gene upstream region contains potential GATA sites at -154, -141, and -60; an E-box at -163; CACCC or GGTGG motifs at -188, -121, and -88; and an AP-1/NF-E2-like site at -42.

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Wang, D. Z., R. S. Reiter, J. L. Lin, Q. Wang, H. S. Williams, S. L. Krob, T. M. Schultheiss, S. Evans, and J. J. Lin. "Requirement of a novel gene, Xin, in cardiac morphogenesis." Development 126, no. 6 (March 15, 1999): 1281–94. http://dx.doi.org/10.1242/dev.126.6.1281.

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A novel gene, Xin, from chick (cXin) and mouse (mXin) embryonic hearts, may be required for cardiac morphogenesis and looping. Both cloned cDNAs have a single open reading frame, encoding proteins with 2,562 and 1,677 amino acids for cXin and mXin, respectively. The derived amino acid sequences share 46% similarity. The overall domain structures of the predicted cXin and mXin proteins, including proline-rich regions, 16 amino acid repeats, DNA-binding domains, SH3-binding motifs and nuclear localization signals, are highly conserved. Northern blot analyses detect a single message of 8.9 and 5.8 kilo base (kb) from both cardiac and skeletal muscle of chick and mouse, respectively. In situ hybridization reveals that the cXin gene is specifically expressed in cardiac progenitor cells of chick embryos as early as stage 8, prior to heart tube formation. cXin continues to be expressed in the myocardium of developing hearts. By stage 15, cXin expression is also detected in the myotomes of developing somites. Immunofluorescence microscopy reveals that the mXin protein is colocalized with N-cadherin and connexin-43 in the intercalated discs of adult mouse hearts. Incubation of stage 6 chick embryos with cXin antisense oligonucleotides results in abnormal cardiac morphogenesis and an alteration of cardiac looping. The myocardium of the affected hearts becomes thickened and tends to form multiple invaginations into the heart cavity. This abnormal cellular process may account in part for the abnormal looping. cXin expression can be induced by bone morphogenetic protein (BMP) in explants of anterior medial mesoendoderm from stage 6 chick embryos, a tissue that is normally non-cardiogenic. This induction occurs following the BMP-mediated induction of two cardiac-restricted transcription factors, Nkx2.5 and MEF2C. Furthermore, either MEF2C or Nkx2.5 can transactivate a luciferase reporter driven by the mXin promoter in mouse fibroblasts. These results suggest that Xin may participate in a BMP-Nkx2.5-MEF2C pathway to control cardiac morphogenesis and looping.

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Hur, Jeong Hwan, Chan Young Kang, Sungjin Lee, Nazia Parveen, Jihyeon Yu, Amen Shamim, Wanki Yoo, et al. "AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation." Nucleic Acids Research, September 1, 2021. http://dx.doi.org/10.1093/nar/gkab728.

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Abstract I-motif or C4 is a four-stranded DNA structure with a protonated cytosine:cytosine base pair (C+:C) found in cytosine-rich sequences. We have found that oligodeoxynucleotides containing adenine and cytosine repeats form a stable secondary structure at a physiological pH with magnesium ion, which is similar to i-motif structure, and have named this structure ‘adenine:cytosine-motif (AC-motif)’. AC-motif contains C+:C base pairs intercalated with putative A+:C base pairs between protonated adenine and cytosine. By investigation of the AC-motif present in the CDKL3 promoter (AC-motifCDKL3), one of AC-motifs found in the genome, we confirmed that AC-motifCDKL3 has a key role in regulating CDKL3 gene expression in response to magnesium. This is further supported by confirming that genome-edited mutant cell lines, lacking the AC-motif formation, lost this regulation effect. Our results verify that adenine-cytosine repeats commonly present in the genome can form a stable non-canonical secondary structure with a non-Watson–Crick base pair and have regulatory roles in cells, which expand non-canonical DNA repertoires.

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Li, Long, Shujuan Xu, Xueyu Peng, Yuzhuo Ji, He Yan, Cheng Cui, Xiaowei Li, et al. "Engineering G-quadruplex aptamer to modulate its binding specificity." National Science Review, August 31, 2020. http://dx.doi.org/10.1093/nsr/nwaa202.

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Abstract The use of aptamers in bioanalytical and biomedical applications exploits their ability to recognize cell surface protein receptors. Targeted therapeutics and theranostics come to mind in this regard. However, protein receptors occur on both cancer and normal cells; as such, aptamers are now taxed with identifying high vs. low levels of protein expression. Inspired by the flexible template mechanism and elegant control of natural nucleic acid-based structures, we report an allosteric regulation strategy for constructing a structure-switching aptamer for enhanced target cell recognition by engineering aptamers with DNA intercalated motifs (i-motifs) responsive to the microenvironment, such as pH. Structure-switching sensitivity can be readily tuned by manipulating i-motif sequences. However, structure-switching sensitivity is difficult to estimate, making it equally difficult to effectively screen modified aptamers with the desired sensitivity. To address this problem, we selected a fluorescent probe capable of detecting G-quadruplex in complicated biological media.

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Xu, Jie, Sharon Barone, Mujan Varasteh Kia, L. Shannon Holliday, Kamyar Zahedi, and Manoocher Soleimani. "Identification of IQGAP1 as a SLC26A4 (Pendrin)-Binding Protein in the Kidney." Frontiers in Molecular Biosciences 9 (May 5, 2022). http://dx.doi.org/10.3389/fmolb.2022.874186.

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Background: Several members of the SLC26A family of transporters, including SLC26A3 (DRA), SLC26A5 (prestin), SLC26A6 (PAT-1; CFEX) and SLC26A9, form multi-protein complexes with a number of molecules (e.g., cytoskeletal proteins, anchoring or adaptor proteins, cystic fibrosis transmembrane conductance regulator, and protein kinases). These interactions provide regulatory signals for these molecules. However, the identity of proteins that interact with the Cl−/HCO3− exchanger, SLC26A4 (pendrin), have yet to be determined. The purpose of this study is to identify the protein(s) that interact with pendrin.Methods: A yeast two hybrid (Y2H) system was employed to screen a mouse kidney cDNA library using the C-terminal fragment of SLC26A4 as bait. Immunofluorescence microscopic examination of kidney sections, as well as co-immunoprecipitation assays, were performed using affinity purified antibodies and kidney protein extracts to confirm the co-localization and interaction of pendrin and the identified binding partners. Co-expression studies were carried out in cultured cells to examine the effect of binding partners on pendrin trafficking and activity.Results: The Y2H studies identified IQ motif-containing GTPase-activating protein 1 (IQGAP1) as a protein that binds to SLC26A4’s C-terminus. Co-immunoprecipitation experiments using affinity purified anti-IQGAP1 antibodies followed by western blot analysis of kidney protein eluates using pendrin-specific antibodies confirmed the interaction of pendrin and IQGAP1. Immunofluorescence microscopy studies demonstrated that IQGAP1 co-localizes with pendrin on the apical membrane of B-intercalated cells, whereas it shows basolateral expression in A-intercalated cells in the cortical collecting duct (CCD). Functional and confocal studies in HEK-293 cells, as well as confocal studies in MDCK cells, demonstrated that the co-transfection of pendrin and IQGAP1 shows strong co-localization of the two molecules on the plasma membrane along with enhanced Cl−/HCO3− exchanger activity.Conclusion: IQGAP1 was identified as a protein that binds to the C-terminus of pendrin in B-intercalated cells. IQGAP1 co-localized with pendrin on the apical membrane of B-intercalated cells. Co-expression of IQGAP1 with pendrin resulted in strong co-localization of the two molecules and increased the activity of pendrin in the plasma membrane in cultured cells. We propose that pendrin’s interaction with IQGAP1 may play a critical role in the regulation of CCD function and physiology, and that disruption of this interaction could contribute to altered pendrin trafficking and/or activity in pathophysiologic states.

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Lv, Jialan, Zhicheng Pan, Jian Chen, Rui Xu, Dongfei Wang, Jiaqi Huang, Yang Dong, et al. "Phosphoproteomic Analysis Reveals Downstream PKA Effectors of AKAP Cypher/ZASP in the Pathogenesis of Dilated Cardiomyopathy." Frontiers in Cardiovascular Medicine 8 (December 13, 2021). http://dx.doi.org/10.3389/fcvm.2021.753072.

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Background: Dilated cardiomyopathy (DCM) is a major cause of heart failure worldwide. The Z-line protein Cypher/Z-band alternatively spliced PDZ-motif protein (ZASP) is closely associated with DCM, both clinically and in animal models. Our earlier work revealed Cypher/ZASP as a PKA-anchoring protein (AKAP) that tethers PKA to phosphorylate target substrates. However, the downstream PKA effectors regulated by AKAP Cypher/ZASP and their relevance to DCM remain largely unknown.Methods and Results: For the identification of candidate PKA substrates, global quantitative phosphoproteomics was performed on cardiac tissue from wild-type and Cypher-knockout mice with PKA activation. A total of 216 phosphopeptides were differentially expressed in the Cypher-knockout mice; 31 phosphorylation sites were selected as candidates using the PKA consensus motifs. Bioinformatic analysis indicated that differentially expressed proteins were enriched mostly in cell adhesion and mRNA processing. Furthermore, the phosphorylation of β-catenin Ser675 was verified to be facilitated by Cypher. This phosphorylation promoted the transcriptional activity of β-catenin, and also the proliferative capacity of cardiomyocytes. Immunofluorescence staining demonstrated that Cypher colocalised with β-catenin in the intercalated discs (ICD) and altered the cytoplasmic distribution of β-catenin. Moreover, the phosphorylation of two other PKA substrates, vimentin Ser72 and troponin I Ser23/24, was suppressed by Cypher deletion.Conclusions: Cypher/ZASP plays an essential role in β-catenin activation via Ser675 phosphorylation, which modulates cardiomyocyte proliferation. Additionally, Cypher/ZASP regulates other PKA effectors, such as vimentin Ser72 and troponin I Ser23/24. These findings establish the AKAP Cypher/ZASP as a signalling hub in the progression of DCM.

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Gully, Benjamin S., Hariprasad Venugopal, Alex J. Fulcher, Zhihui Fu, Jessica Li, Felix A. Deuss, Carmen Llerena, et al. "The cryo-EM structure of the endocytic receptor DEC-205." Journal of Biological Chemistry, November 30, 2020, jbc.RA120.016451. http://dx.doi.org/10.1074/jbc.ra120.016451.

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DEC-205 (CD205), a member of the macrophage mannose receptor protein family, is the prototypic endocytic receptor of dendritic cells, whose ligands include phosphorothioated cytosine-guanosine (CpG) oligonucleotides, a motif often seen in bacterial or viral DNA. However, despite growing biological and clinical significance, little is known about the structural arrangement of this receptor or any of its family members. Here we describe the 3.2 Å cryo-EM structure of human DEC-205, thereby illuminating the structure of the mannose receptor protein family. The DEC-205 monomer forms a compact structure comprising two intercalated rings of C-type lectin-like domains, where the N-terminal cysteine-rich and fibronectin domains reside at the central intersection. We establish a pH dependant oligomerisation pathway forming tetrameric DEC-205 using solution-based techniques and ultimately solved the 4.9 Å cryo-EM structure of the DEC-205 tetramer to identify the unfurling of the second lectin ring which enables tetramer formation. Furthermore, we suggest the relevance of this oligomerisation pathway within a cellular setting, whereby CpG binding appeared to disrupt this cell-surface oligomer. Accordingly, we provide insight into the structure and oligomeric assembly of the DEC-205 receptor.

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Khamari, Laxmikanta, and Saptarshi Mukherjee. "Deciphering the Nanoconfinement Effect on the Folding Pathway of c-MYC Promoter-Based Intercalated-Motif DNA by Single-Molecule Förster Resonance Energy Transfer." Journal of Physical Chemistry Letters, August 25, 2022, 8169–76. http://dx.doi.org/10.1021/acs.jpclett.2c01893.

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Jamroskovic, Jan, Marco Deiana, and Nasim Sabouri. "Probing the folding pathways of four-stranded intercalated cytosine-rich motifs at single base-pair resolution." Biochimie, April 2022. http://dx.doi.org/10.1016/j.biochi.2022.04.007.

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Journal articles on the topic 'Intercalated Motif'

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